[Gate-users] Simulate a beam with spaced bunches in GATE

Salvatore Di Guida salvatore.di.guida at cern.ch
Tue May 14 18:37:22 CEST 2013


Hi!
Sorry for replying just now. I made the patch I attached before and started doing my simulations and analysis...

Regarding the source. I do not think it is worth adding a new source: the feature of the bunches can be enabled in Geant4 with GPS [1], so it would be better to enable GATE to use it. I think it would be useful to add this feature both to the controls of the GPS source, as well as in the PBS source provided by GATE.
I can try to implement them, if I have some time...

Best regards

Salvatore

[1] Dummy interface (built in 5 minutes after a quick reading of GPS documentation and tutorials):
class BunchedPrimaryGeneratorAction : public G4VUserPrimaryGeneratorAction
{
  public:
    BunchedPrimaryGeneratorAction(
      const G4String& particleName = "bunchino",
      G4double energy = 1.*MeV,
      G4ThreeVector position= G4ThreeVector(0,0,0),
      G4ThreeVector momentumDirection = G4ThreeVector(0,0,1));    
    ~BunchedPrimaryGeneratorAction();

    // methods
    virtual void GeneratePrimaries(G4Event*);

  private:
    // data members
    G4GeneralParticleSource fParticleSource; // Own a GPS object (easier) - or you can have a pointer
};

void BunchedPrimaryGeneratorAction::GeneratePrimaries(G4Event* anEvent)
{
  // this function is called at the begining of event

  fParticleGun->GeneratePrimaryVertex(anEvent);
  // Look inside the event and change the time of primaries according to your needs ... 
}
________________________________________
From: gate-users-bounces at lists.opengatecollaboration.org [gate-users-bounces at lists.opengatecollaboration.org] on behalf of Salvatore Di Guida [salvatore.di.guida at cern.ch]
Sent: 14 May 2013 18:21
To: David Sarrut; Irene Torres
Cc: gate-users
Subject: Re: [Gate-users] Simulate a beam with spaced bunches in GATE

Hi Robert!
As I said in my previous mail, I am currently using Gate v6.1. I adapted the phase space actor for that release, and patched my version using the patch file in attachment. I tested it, it just works.
Anyhow, it would be great to see the development trunk of GATE. Which VCS (SVN, Mercurial, Git) do the GATE developers use? Can users be granted access to the repository? If so, which is the address?

Thanks

Salvatore

________________________________
From: david.sarrut at gmail.com [david.sarrut at gmail.com] on behalf of David Sarrut [David.Sarrut at creatis.insa-lyon.fr]
Sent: 10 May 2013 09:13
To: Irene Torres; Salvatore Di Guida
Cc: robert at imnc.in2p3.fr; Dubois Albertine; gate-users
Subject: Re: [Gate-users] Simulate a beam with spaced bunches in GATE

Hello Irene and Salvatore,

the enhanced phase space actor is in the develop part of the current gate repository and you will be able to access to this current development version (without guarantee) in some times, but we still need to setup correctly the system, so please be patient. In the meantime, you can look at the code and try to modify the classes GatePhaseSpaceActor.

Sincerely,
David


On Mon, Apr 29, 2013 at 9:08 PM, Irene Torres <ireneta at ific.uv.es<mailto:ireneta at ific.uv.es>> wrote:
Hello David,

Thank you for your help!

I have tried the last option you suggested and I got an error during GATE compilation:

./tmp/Linux-g++/Gate/libGate.so: undefined reference to `GatePhaseSpaceActor::GatePhaseSpaceActor(G4String, int)'
collect2: ld returned 1 exit status
make: *** [bin/Linux-g++/Gate] Error 1
root at cormorant:/opt/OpenGate6/gate_v6.1#<mailto:root at cormorant:/opt/OpenGate6/gate_v6.1#> exit

Any idea where I should start searching??
Thanks again!

Cheers,

Irene


On 04/29/2013 08:00 AM, David Sarrut wrote:
Hello Salvatore,

I haven't got the time to look at in detail, but this is true that phase-space dose not store runID, eventID, and that, in that case, the time is no taken into account with the source.

I think the best solution for your problem is to write a new type of source. That should not be too difficult (even if it requires some times), starting from a new class inheriting from GateVSource. You will need also to slightly modify GateSourceMgr (in function AddSource) to enable your new source type. Maybe instead of a new source type, you can alternatively add timing option to the GPS source type. I am convinced that it could be useful to other too.

Another alternative option, simpler but maybe not as useful, could be to add RunID and EvenID branch in the phase space. I attached to this mail a new version of the PhaseSpaceActor that store eventID and runID. You can try it (without any guarantee) by adding the files in the src/include folders of the digits_hits folder.

Sincerely,
David


On Mon, Apr 22, 2013 at 5:58 PM, Salvatore Di Guida <salvatore.di.guida at cern.ch<mailto:salvatore.di.guida at cern.ch>> wrote:
Dear GATE users and developers,
since I have been using the framework for few weeks, I apologize for my misunderstandings and mistakes.
I have simulated the detector I am working on as two water boxes (equivalent to gas detectors), two plastic scintillator boxes plus a scanner system made up of 30 plastic scintillators. I have attached one phase space to each water box (in order to describe the incoming particles from the source and from the first box, respectively), to the air box between the water boxes (in order to look at the particles outgoing the first water box) and to the air box between the second water fox and the first scintillator (in order to look at the particles outgoing the second water box). Moreover, I have defined a proton pencil beam source: I have implemented it both via G4 GeneralParticleSource and using the PencilBeam template in GATE.
If you like, you can check the geometry and the sources in details in the archive I am attaching to this mail: there you can find the macros I am using. I am working with GATE 6.1 on vGATE 2.0.
The output I want to retrieve is, for each proton, the x and y position in each water box, and the energy deposition in each level of the scanner system.
In my first attempt, I simply created the geometry, the source, and the digitizer system, and launched the simulation with 1000 primaries, producing ROOT files as output. My idea was to distinguish the incoming protons by the (runID, eventID) pair: unfortunately, the phase space does not store this piece of information [1].
Then, since both the phase space and the scanner keep time information, my next attempt was to calculate the coincidences of each proton in the water boxes and in the first scintillator: in this way, I could mark the protons propagating outside the scanner with the same (runID, eventID) pair established inside it. Unfortunately, both sources generate all the protons at t = 0, so it is impossible to get an adequate result via coincidence computations [2].
Next, I tried to overcome this issue using time slices in Data Acquisition: I defined 1000 time slices, where each slice has a time duration larger than the time of flight of the proton, so that I had one primary per slice, and the association between data in water and data in the scanner could be quite easy. Unfortunately, when the second time slice starts, GATE crashes with a segmentation violation with both the PencilBeam source and with GPS source (even when I tried to set GeneralParticleSource::number or setActivity in GATE). Debugging with gdb did not help.

My question is: is there a way in GATE to produce a beam source where a given number of protons are grouped in bunches spaced by a given time interval (say: 100 protons-per-bunch, bunches spaced by 100 ms).

Thanks in advance for your help!

Salvatore

[1]
$ root -l
root [] TFile* gem0RootFile = TFile::Open("GEM0PHS_1000primaries_perfectPBS.root")
root [] TTree* gem0PhaseSpaceTree = (TTree*) gem0RootFile->Get( "PhaseSpace" )
root [] phaseSpaceTree->Print()

[2] the source is 0.05 mm far from the phase space, which is at the origin of the world; so, all protons enter the water box associated to the phase space at t > 0:
root [] TFile* gem0RootFile = TFile::Open("GEM0PHS_1000primaries_perfectPBS.root")
root [] TTree* gem0PhaseSpaceTree = (TTree*) gem0RootFile->Get( "PhaseSpace" )
root [] gem0PhaseSpaceTree->Scan( "ParticleName:Time:X:Y:Z:dX:dY:dZ:Ekine" )
************************************************************************************************************************
*    Row   * ParticleN *      Time *         X *         Y *         Z *        dX *        dY *        dZ *     Ekine *
************************************************************************************************************************
*        0 *    proton * 0.0003519 *         0 *         0 *         0 * -2.63e-08 * 2.610e-08 *         1 *       100 *
*        1 *    proton * 0.0003519 *         0 *         0 *         0 * 2.421e-08 * 9.183e-11 *         1 *       100 *
*        2 *    proton * 0.0003519 *         0 *         0 *         0 * 1.011e-09 * 2.843e-09 *         1 *       100 *
*        3 *    proton * 0.0003519 *         0 *         0 *         0 * -5.11e-09 * 7.478e-10 *         1 *       100 *
*        4 *    proton * 0.0003519 *         0 *         0 *         0 * 2.031e-08 * -2.61e-08 *         1 *       100 *
*        5 *    proton * 0.0003519 *         0 *         0 *         0 * 2.153e-08 * 9.473e-09 *         1 *       100 *
...
And here it is how the ROOT file for the phase space between the two water boxes look like: there is a very slight difference in timing between protons...
root [] TFile* gemSpacingRootFile = TFile::Open("GEMSpacingPHS_1000primaries_perfectPBS.root")
root [] TTree* gemSpacingPhaseSpaceTree = (TTree*) gemSpacingRootFile->Get( "PhaseSpace" )
root [] gemSpacingPhaseSpaceTree->Scan( "ParticleName:Time:X:Y:Z:dX:dY:dZ:Ekine" )
************************************************************************************************************************
*    Row   * ParticleN *      Time *         X *         Y *         Z *        dX *        dY *        dZ *     Ekine *
************************************************************************************************************************
*        0 *    proton * 0.0194233 * 0.0030443 * -0.001321 * 2.7000000 * 0.0042755 * -0.001657 * 0.9999895 * 98.147529 *
*        1 *    proton * 0.0194286 * -0.002575 * 0.0078605 * 2.7000000 * -0.002732 * 0.0060394 * 0.9999780 * 97.927230 *
*        2 *    proton * 0.0194189 * 0.0081350 * -0.003375 * 2.7000000 * 0.0061967 * -0.000981 * 0.9999803 * 98.123619 *
*        3 *    proton * 0.0194209 * 0.0102742 * -0.006316 * 2.7000000 * -0.002067 * -0.004013 * 0.9999898 * 97.984443 *
*        4 *    proton * 0.0194191 * -0.007278 * 0.0019697 * 2.7000000 * -0.005616 * 0.0024906 * 0.9999811 * 98.163551 *
...

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--
David Sarrut, Phd
Chargé de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut<http://www.creatis.insa-lyon.fr/%7Edsarrut>
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
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--
David Sarrut, Phd
Chargé de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
_________________________________


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